Coexpression cluster:C31
From FANTOM5_SSTAR
Full id: C31_skeletal_tongue_diaphragm_throat_penis_skin_trachea
Phase1 CAGE Peaks
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 8.83424747068594e-06 | 0.000621342072104911 | 5 | 65 | Glycolysis / Gluconeogenesis (KEGG):00010 |
| 0.000230755522774235 | 0.0121723538263409 | 3 | 28 | Pentose phosphate pathway (KEGG):00030 |
| 0.000490549199328691 | 0.0172509801763923 | 3 | 36 | Fructose and mannose metabolism (KEGG):00051 |
| 1.15065548619832e-05 | 0.000728364922763534 | 7 | 177 | Calcium signaling pathway (KEGG):04020 |
| 0.000324787990025204 | 0.0137060531790636 | 6 | 214 | Regulation of actin cytoskeleton (KEGG):04810 |
| 0.00032348489368837 | 0.0137060531790636 | 5 | 138 | Insulin signaling pathway (KEGG):04910 |
| 6.94517014469367e-08 | 1.09907317539777e-05 | 7 | 83 | Hypertrophic cardiomyopathy (HCM) (KEGG):05410 |
| 1.67087028361086e-05 | 0.000961509899568795 | 5 | 74 | Arrhythmogenic right ventricular cardiomyopathy (ARVC) (KEGG):05412 |
| 2.50054283301031e-06 | 0.000226120516185075 | 6 | 90 | Dilated cardiomyopathy (KEGG):05414 |
| 0.000261000163731931 | 0.0127087002801779 | 4 | 72 | Viral myocarditis (KEGG):05416 |
| 8.29818804261411e-18 | 5.25275303097473e-15 | 11 | 39 | Striated Muscle Contraction (Wikipathways):WP383 |
| 0.000490549199328691 | 0.0172509801763923 | 3 | 36 | Glycogen Metabolism (Wikipathways):WP500 |
| 1.94066461930908e-06 | 0.000204740117337108 | 5 | 48 | Glycolysis and Gluconeogenesis (Wikipathways):WP534 |
| 0.0004598136126461 | 0.0172509801763923 | 5 | 149 | Calcium Regulation in the Cardiac Cell (Wikipathways):WP536 |
| 1.21380856377035e-06 | 0.000153668164173326 | 7 | 126 | Metabolism of carbohydrates (Reactome):REACT_474 |
| 9.96609072137847e-15 | 3.15426771331629e-12 | 10 | 49 | Muscle contraction (Reactome):REACT_17044 |
| 1.8576297395608e-12 | 3.91959875047329e-10 | 15 | 288 | {ACTB,297} (Static Module):NA |
| 7.9846704657637e-06 | 0.000621342072104911 | 4 | 30 | {CALM1,30} (Static Module):NA |
| 0.000797154160384212 | 0.0265578201854319 | 2 | 10 | {SPTAN1,10} (Static Module):NA |
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0006936 | muscle contraction | 9.98564168682262e-26 |
| GO:0003012 | muscle system process | 9.98564168682262e-26 |
| GO:0006941 | striated muscle contraction | 8.43668432021435e-22 |
| GO:0044449 | contractile fiber part | 7.82061514597761e-21 |
| GO:0043292 | contractile fiber | 1.70907813894243e-20 |
| GO:0030017 | sarcomere | 2.95410035928916e-18 |
| GO:0030016 | myofibril | 9.57548209589633e-18 |
| GO:0015629 | actin cytoskeleton | 4.17810766825591e-15 |
| GO:0008092 | cytoskeletal protein binding | 2.67683456297195e-12 |
| GO:0005856 | cytoskeleton | 6.4458716119872e-11 |
| GO:0032501 | multicellular organismal process | 9.94445886325297e-11 |
| GO:0007517 | muscle development | 3.98116535402961e-10 |
| GO:0005737 | cytoplasm | 7.50610936751503e-10 |
| GO:0008307 | structural constituent of muscle | 2.87218009273304e-09 |
| GO:0043228 | non-membrane-bound organelle | 3.89499382522904e-09 |
| GO:0043232 | intracellular non-membrane-bound organelle | 3.89499382522904e-09 |
| GO:0005865 | striated muscle thin filament | 4.76350863304534e-09 |
| GO:0005859 | muscle myosin complex | 4.76350863304534e-09 |
| GO:0016528 | sarcoplasm | 4.76350863304534e-09 |
| GO:0016529 | sarcoplasmic reticulum | 4.76350863304534e-09 |
| GO:0016460 | myosin II complex | 5.8830992883799e-09 |
| GO:0044444 | cytoplasmic part | 1.55362370609148e-07 |
| GO:0003008 | system process | 2.51299624653359e-07 |
| GO:0005515 | protein binding | 2.61610679275086e-07 |
| GO:0003779 | actin binding | 3.41752721189633e-07 |
| GO:0033017 | sarcoplasmic reticulum membrane | 5.23311639576676e-07 |
| GO:0006937 | regulation of muscle contraction | 3.7982353108975e-06 |
| GO:0044430 | cytoskeletal part | 3.8517072288738e-06 |
| GO:0032982 | myosin filament | 3.87546861584246e-06 |
| GO:0005863 | striated muscle thick filament | 3.87546861584246e-06 |
| GO:0005861 | troponin complex | 1.41637729319868e-05 |
| GO:0030239 | myofibril assembly | 2.25491720235153e-05 |
| GO:0055001 | muscle cell development | 2.25491720235153e-05 |
| GO:0055002 | striated muscle cell development | 2.25491720235153e-05 |
| GO:0016459 | myosin complex | 2.2680300526239e-05 |
| GO:0045445 | myoblast differentiation | 3.03457966478371e-05 |
| GO:0006942 | regulation of striated muscle contraction | 3.3079483205872e-05 |
| GO:0007519 | skeletal muscle development | 4.22947913151449e-05 |
| GO:0048628 | myoblast maturation | 6.6950110764492e-05 |
| GO:0048627 | myoblast development | 8.95550170708193e-05 |
| GO:0005516 | calmodulin binding | 9.65251195678146e-05 |
| GO:0014706 | striated muscle development | 0.000147523826938479 |
| GO:0048741 | skeletal muscle fiber development | 0.000152859227770121 |
| GO:0048747 | muscle fiber development | 0.000152859227770121 |
| GO:0044424 | intracellular part | 0.00017665504818708 |
| GO:0048513 | organ development | 0.00017665504818708 |
| GO:0042692 | muscle cell differentiation | 0.000206678933241389 |
| GO:0005977 | glycogen metabolic process | 0.000220679214609914 |
| GO:0006073 | glucan metabolic process | 0.000235274263008101 |
| GO:0051146 | striated muscle cell differentiation | 0.000240459735380112 |
| GO:0048856 | anatomical structure development | 0.000244562570162515 |
| GO:0006112 | energy reserve metabolic process | 0.000382252641868833 |
| GO:0005523 | tropomyosin binding | 0.000522930133095587 |
| GO:0031032 | actomyosin structure organization and biogenesis | 0.000522930133095587 |
| GO:0043234 | protein complex | 0.000560546245815447 |
| GO:0005884 | actin filament | 0.00086428498905539 |
| GO:0044446 | intracellular organelle part | 0.00147127288825896 |
| GO:0048731 | system development | 0.00150078329047224 |
| GO:0044422 | organelle part | 0.00150078329047224 |
| GO:0044264 | cellular polysaccharide metabolic process | 0.00175094554430813 |
| GO:0005976 | polysaccharide metabolic process | 0.00185638690527584 |
| GO:0005509 | calcium ion binding | 0.00185638690527584 |
| GO:0044262 | cellular carbohydrate metabolic process | 0.00185906293921157 |
| GO:0005622 | intracellular | 0.00233499664924776 |
| GO:0007275 | multicellular organismal development | 0.00263597684959727 |
| GO:0017022 | myosin binding | 0.00308538970765157 |
| GO:0006006 | glucose metabolic process | 0.0037880074655374 |
| GO:0048469 | cell maturation | 0.00420027085790783 |
| GO:0016012 | sarcoglycan complex | 0.00472412621787776 |
| GO:0015980 | energy derivation by oxidation of organic compounds | 0.00533792347619993 |
| GO:0021700 | developmental maturation | 0.00652292046939437 |
| GO:0051924 | regulation of calcium ion transport | 0.00652292046939437 |
| GO:0016011 | dystroglycan complex | 0.00652292046939437 |
| GO:0006096 | glycolysis | 0.00729105835872223 |
| GO:0030018 | Z disc | 0.00871896383390033 |
| GO:0044459 | plasma membrane part | 0.00891108099993321 |
| GO:0000146 | microfilament motor activity | 0.00977947388672997 |
| GO:0006007 | glucose catabolic process | 0.0100338734116727 |
| GO:0030036 | actin cytoskeleton organization and biogenesis | 0.0100338734116727 |
| GO:0044432 | endoplasmic reticulum part | 0.0110996208066196 |
| GO:0016866 | intramolecular transferase activity | 0.0117042253621655 |
| GO:0031674 | I band | 0.0117042253621655 |
| GO:0043269 | regulation of ion transport | 0.0117042253621655 |
| GO:0030029 | actin filament-based process | 0.011844812953703 |
| GO:0019320 | hexose catabolic process | 0.0119651436666855 |
| GO:0046365 | monosaccharide catabolic process | 0.0121131138559424 |
| GO:0046164 | alcohol catabolic process | 0.0125558727688723 |
| GO:0019318 | hexose metabolic process | 0.0131341803591883 |
| GO:0005996 | monosaccharide metabolic process | 0.0140791013851807 |
| GO:0051239 | regulation of multicellular organismal process | 0.0146021470431144 |
| GO:0016010 | dystrophin-associated glycoprotein complex | 0.0179522263933388 |
| GO:0043229 | intracellular organelle | 0.0183540745972316 |
| GO:0043226 | organelle | 0.0183776908724005 |
| GO:0006000 | fructose metabolic process | 0.0189531811478071 |
| GO:0032502 | developmental process | 0.0189531811478071 |
| GO:0005200 | structural constituent of cytoskeleton | 0.0189531811478071 |
| GO:0006816 | calcium ion transport | 0.0201423987196451 |
| GO:0044275 | cellular carbohydrate catabolic process | 0.0202303858079202 |
| GO:0042995 | cell projection | 0.0202303858079202 |
| GO:0005789 | endoplasmic reticulum membrane | 0.0202303858079202 |
| GO:0016052 | carbohydrate catabolic process | 0.0202303858079202 |
| GO:0043167 | ion binding | 0.0202303858079202 |
| GO:0014819 | regulation of skeletal muscle contraction | 0.0202303858079202 |
| GO:0045199 | maintenance of epithelial cell polarity | 0.0202303858079202 |
| GO:0014724 | regulation of twitch skeletal muscle contraction | 0.0202303858079202 |
| GO:0031443 | fast-twitch skeletal muscle fiber contraction | 0.0202303858079202 |
| GO:0043033 | isoamylase complex | 0.0202303858079202 |
| GO:0046314 | phosphocreatine biosynthetic process | 0.0202303858079202 |
| GO:0031448 | positive regulation of fast-twitch skeletal muscle contraction | 0.0202303858079202 |
| GO:0004679 | AMP-activated protein kinase activity | 0.0202303858079202 |
| GO:0031446 | regulation of fast-twitch skeletal muscle contraction | 0.0202303858079202 |
| GO:0003010 | voluntary skeletal muscle contraction | 0.0202303858079202 |
| GO:0045989 | positive regulation of striated muscle contraction | 0.0202303858079202 |
| GO:0014721 | twitch skeletal muscle contraction | 0.0202303858079202 |
| GO:0032236 | positive regulation of calcium ion transport via store-operated calcium channel | 0.0202303858079202 |
| GO:0006603 | phosphocreatine metabolic process | 0.0202303858079202 |
| GO:0030507 | spectrin binding | 0.0202303858079202 |
| GO:0032237 | activation of store-operated calcium channel activity | 0.0202303858079202 |
| GO:0043536 | positive regulation of blood vessel endothelial cell migration | 0.0202303858079202 |
| GO:0042175 | nuclear envelope-endoplasmic reticulum network | 0.0209269994505625 |
| GO:0005975 | carbohydrate metabolic process | 0.0210241118688545 |
| GO:0051091 | positive regulation of transcription factor activity | 0.024615447573797 |
| GO:0044464 | cell part | 0.0279694082269571 |
| GO:0051049 | regulation of transport | 0.0301000463414239 |
| GO:0007010 | cytoskeleton organization and biogenesis | 0.0328403145624998 |
| GO:0009982 | pseudouridine synthase activity | 0.0332050135306425 |
| GO:0050881 | musculoskeletal movement | 0.0332050135306425 |
| GO:0030240 | muscle thin filament assembly | 0.0332050135306425 |
| GO:0004052 | arachidonate 12-lipoxygenase activity | 0.0332050135306425 |
| GO:0035025 | positive regulation of Rho protein signal transduction | 0.0332050135306425 |
| GO:0008184 | glycogen phosphorylase activity | 0.0332050135306425 |
| GO:0043532 | angiostatin binding | 0.0332050135306425 |
| GO:0051373 | FATZ binding | 0.0332050135306425 |
| GO:0032234 | regulation of calcium ion transport via store-operated calcium channel | 0.0332050135306425 |
| GO:0003009 | skeletal muscle contraction | 0.0332050135306425 |
| GO:0050879 | multicellular organismal movement | 0.0332050135306425 |
| GO:0035090 | maintenance of apical/basal cell polarity | 0.0332050135306425 |
| GO:0004134 | 4-alpha-glucanotransferase activity | 0.0332050135306425 |
| GO:0004133 | glycogen debranching enzyme activity | 0.0332050135306425 |
| GO:0043270 | positive regulation of ion transport | 0.0332050135306425 |
| GO:0042132 | fructose-bisphosphatase activity | 0.0332050135306425 |
| GO:0030011 | maintenance of cell polarity | 0.0332050135306425 |
| GO:0004135 | amylo-alpha-1,6-glucosidase activity | 0.0332050135306425 |
| GO:0047977 | hepoxilin-epoxide hydrolase activity | 0.0332050135306425 |
| GO:0051928 | positive regulation of calcium ion transport | 0.0332050135306425 |
| GO:0005605 | basal lamina | 0.0361715372844985 |
| GO:0005783 | endoplasmic reticulum | 0.0361715372844985 |
| GO:0005178 | integrin binding | 0.0374758610374373 |
| GO:0015674 | di-, tri-valent inorganic cation transport | 0.0375905862461542 |
| GO:0032991 | macromolecular complex | 0.0412271747726947 |
| GO:0009451 | RNA modification | 0.0440014867280487 |
| GO:0006811 | ion transport | 0.0453804946057911 |
| GO:0051393 | alpha-actinin binding | 0.0453804946057911 |
| GO:0043535 | regulation of blood vessel endothelial cell migration | 0.0453804946057911 |
| GO:0006599 | phosphagen metabolic process | 0.0453804946057911 |
| GO:0014866 | skeletal myofibril assembly | 0.0453804946057911 |
| GO:0050682 | AF-2 domain binding | 0.0453804946057911 |
| GO:0016556 | mRNA modification | 0.0453804946057911 |
| GO:0042396 | phosphagen biosynthetic process | 0.0453804946057911 |
| GO:0046872 | metal ion binding | 0.0480284272662177 |
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br>disease_data<br>
| Ontology term | p-value | n |
|---|---|---|
| vascular disease | 3.25e-09 | 1 |
| ischemia | 3.25e-09 | 1 |
| extrinsic cardiomyopathy | 3.25e-09 | 1 |
| myocardial ischemia | 3.25e-09 | 1 |
| myocardial infarction | 3.25e-09 | 1 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 3.15314e-05 |
| MA0004.1 | 0.00024451 |
| MA0006.1 | 0.113464 |
| MA0007.1 | 0.718356 |
| MA0009.1 | 0.0215793 |
| MA0014.1 | 1.123e-08 |
| MA0017.1 | 1.21192 |
| MA0019.1 | 1.00098 |
| MA0024.1 | 0.00344018 |
| MA0025.1 | 0.0171398 |
| MA0027.1 | 0.721342 |
| MA0028.1 | 1.79578e-08 |
| MA0029.1 | 0.155266 |
| MA0030.1 | 0.00404851 |
| MA0031.1 | 0.0309709 |
| MA0038.1 | 0.000109752 |
| MA0040.1 | 0.014552 |
| MA0041.1 | 0.0657808 |
| MA0042.1 | 0.0769929 |
| MA0043.1 | 0.00809539 |
| MA0046.1 | 0.08012 |
| MA0048.1 | 1.95645 |
| MA0050.1 | 2.07395e-05 |
| MA0051.1 | 2.94529e-05 |
| MA0052.1 | 7.57916 |
| MA0055.1 | 1.73637 |
| MA0056.1 | 0 |
| MA0057.1 | 0.139613 |
| MA0058.1 | 0.000105654 |
| MA0059.1 | 0.123619 |
| MA0060.1 | 4.54116e-05 |
| MA0061.1 | 0.000626868 |
| MA0063.1 | 0 |
| MA0066.1 | 2.08213 |
| MA0067.1 | 0.0973154 |
| MA0068.1 | 0.000403689 |
| MA0069.1 | 0.315147 |
| MA0070.1 | 0.404943 |
| MA0071.1 | 4.50102 |
| MA0072.1 | 1.09951 |
| MA0073.1 | 10.5989 |
| MA0074.1 | 1.79114 |
| MA0076.1 | 5.93694e-08 |
| MA0077.1 | 0.0119542 |
| MA0078.1 | 0.986109 |
| MA0081.1 | 0.0557964 |
| MA0083.1 | 1.37061 |
| MA0084.1 | 0.0288413 |
| MA0087.1 | 0.108851 |
| MA0088.1 | 1.54875 |
| MA0089.1 | 0 |
| MA0090.1 | 0.219177 |
| MA0091.1 | 3.81047 |
| MA0092.1 | 2.98896 |
| MA0093.1 | 1.01873e-05 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.029816 |
| MA0101.1 | 0.00715404 |
| MA0103.1 | 2.4403 |
| MA0105.1 | 0.348176 |
| MA0106.1 | 0.0118763 |
| MA0107.1 | 0.00424413 |
| MA0108.2 | 0.280325 |
| MA0109.1 | 0 |
| MA0111.1 | 0.67122 |
| MA0113.1 | 1.29858 |
| MA0114.1 | 1.876 |
| MA0115.1 | 3.05319 |
| MA0116.1 | 0.195147 |
| MA0117.1 | 0.0143377 |
| MA0119.1 | 1.11319 |
| MA0122.1 | 0.571883 |
| MA0124.1 | 0.675251 |
| MA0125.1 | 0.0386054 |
| MA0130.1 | 0 |
| MA0131.1 | 0.0102783 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.316509 |
| MA0136.1 | 0.000147435 |
| MA0139.1 | 0.000545477 |
| MA0140.1 | 0.00328865 |
| MA0141.1 | 0.893629 |
| MA0142.1 | 0.137536 |
| MA0143.1 | 0.36424 |
| MA0144.1 | 0.0304494 |
| MA0145.1 | 0.0906225 |
| MA0146.1 | 0.00526631 |
| MA0147.1 | 0.000107128 |
| MA0148.1 | 0.293744 |
| MA0149.1 | 0.138458 |
| MA0062.2 | 2.87136e-07 |
| MA0035.2 | 0.0105871 |
| MA0039.2 | 0.000285477 |
| MA0138.2 | 0.698464 |
| MA0002.2 | 0.0476325 |
| MA0137.2 | 0.0224495 |
| MA0104.2 | 5.25368e-07 |
| MA0047.2 | 0.314774 |
| MA0112.2 | 8.37512 |
| MA0065.2 | 4.08372 |
| MA0150.1 | 0.191159 |
| MA0151.1 | 0 |
| MA0152.1 | 0.670513 |
| MA0153.1 | 0.713649 |
| MA0154.1 | 0.568827 |
| MA0155.1 | 7.57139 |
| MA0156.1 | 1.3649e-08 |
| MA0157.1 | 0.0915477 |
| MA0158.1 | 0 |
| MA0159.1 | 2.75961 |
| MA0160.1 | 0.881688 |
| MA0161.1 | 0 |
| MA0162.1 | 6.05783e-08 |
| MA0163.1 | 5.53153 |
| MA0164.1 | 0.095748 |
| MA0080.2 | 1.99739e-06 |
| MA0018.2 | 0.0360873 |
| MA0099.2 | 0.00770718 |
| MA0079.2 | 0.0395186 |
| MA0102.2 | 0.0366105 |
| MA0258.1 | 7.12833 |
| MA0259.1 | 0.000381418 |
| MA0442.1 | 0 |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| SUZ12#23512 | 60 | 5.24772574984952 | 4.26912361552114e-25 | 1.36349541676273e-22 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
